Stoner has swapped the red of Ducati for the orange of Repsol Honda
Casey Stoner broke the lap record at Malaysia's Sepang circuit to end the final MotoGP pre-season test on a high.
The Repsol Honda rider set a new record of one minute 59.665 and team-mate Dani Pedrosa also went under two minutes.
But defending champion Jorge Lorenzo could only finish in seventh, while Britain's Cal Crutchlow was 14th.
Stoner said: "I'm feeling more and more comfortable on the bike and I can't wait to get to Qatar for the first race."
Honda Gresini's Marco Simoncelli was third in testing, with the third Repsol rider, Andrea Dovizioso, in fourth, and Yamaha Factory Racing's Ben Spies next.
Valentino Rossi, continuing his comeback after a shoulder injury and preparing for his first race on the Ducati, was almost two seconds slower than Stoner. He finished in 11th place, though this was an improvement from 13th in testing earlier in February.
Stoner, the Australian who won the title in 2007, said: "The test here has been very productive for us, we did a long run here today - almost race distance - and gathered some key information."
I was happy to have improved some things with the bike
Lorenzo felt "quite tired" after finishing the two and a half days of testing with a 20-lap run.
But he said his Yamaha Factory Racing team had "a very consistent pace" and added: "I was happy to have improved some things with the bike."
Coventry-born Crutchlow, the sole British rider in MotoGP, will make his debut with the Monster Yamaha Tech 3 team in Qatar on 20 March.
The BBC will cover qualifying and all the season's races on television, the red button and on the BBC Sport website.